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- PDB-5roo: PanDDA analysis group deposition -- Proteinase K crystal structur... -

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Basic information

Entry
Database: PDB / ID: 5roo
TitlePanDDA analysis group deposition -- Proteinase K crystal structure Apo73
ComponentsProteinase K
KeywordsHYDROLASE / FragMAX / FragMAXapp / fragment screening / inhibition
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / : / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / : / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.41 Å
AuthorsLima, G.M.A. / Talibov, V. / Benz, L.S. / Jagudin, E. / Mueller, U.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-06454 Sweden
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: FragMAXapp: crystallographic fragment-screening data-analysis and project-management system.
Authors: Lima, G.M.A. / Jagudin, E. / Talibov, V.O. / Benz, L.S. / Marullo, C. / Barthel, T. / Wollenhaupt, J. / Weiss, M.S. / Mueller, U.
History
DepositionSep 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_radiation_wavelength / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0552
Polymers28,9591
Non-polymers961
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.640, 68.640, 106.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1174-

HOH

21A-1338-

HOH

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Components

#1: Protein Proteinase K / Endopeptidase K / Tritirachium alkaline proteinase


Mass: 28958.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parengyodontium album (fungus) / Gene: PROK / Production host: Escherichia coli (E. coli) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.39 % / Mosaicity: 0 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.2M ammonium sulfate, 0.1M Tris-HCl, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.41→57.75 Å / Num. obs: 42238 / % possible obs: 85 % / Redundancy: 1 % / Net I/σ(I): 12.7 / Num. measured all: 42238
Reflection shell
Resolution (Å)Redundancy (%)Num. measured allNum. unique obsDiffraction-IDNet I/σ(I) obs% possible all
1.41-1.44152052011.421.3
7.6-57.751389389134.599.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.25 Å57.75 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→48.54 Å / SU ML: 0.1969 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.2656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2219 2042 4.84 %
Rwork0.2007 40189 -
obs0.2017 42231 84.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.54 Å2
Refinement stepCycle: LAST / Resolution: 1.41→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 5 292 2320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592066
X-RAY DIFFRACTIONf_angle_d0.83142810
X-RAY DIFFRACTIONf_chiral_restr0.078312
X-RAY DIFFRACTIONf_plane_restr0.006370
X-RAY DIFFRACTIONf_dihedral_angle_d5.5672307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.440.2983480.2901684X-RAY DIFFRACTION22.45
1.44-1.480.3011550.28061065X-RAY DIFFRACTION34.49
1.48-1.520.3314770.28461480X-RAY DIFFRACTION47.47
1.52-1.570.27091040.26432254X-RAY DIFFRACTION72.35
1.57-1.620.28371530.28242898X-RAY DIFFRACTION94.02
1.62-1.670.30941590.30013127X-RAY DIFFRACTION99.55
1.67-1.740.31191590.28843100X-RAY DIFFRACTION100
1.74-1.820.27521500.27323125X-RAY DIFFRACTION99.97
1.82-1.920.29681720.24083134X-RAY DIFFRACTION100
1.92-2.040.25151680.22623123X-RAY DIFFRACTION100
2.04-2.190.21581650.20113165X-RAY DIFFRACTION99.97
2.19-2.410.221480.19033171X-RAY DIFFRACTION99.97
2.41-2.760.20721590.19183204X-RAY DIFFRACTION99.97
2.76-3.480.21261700.18813224X-RAY DIFFRACTION100
3.48-48.540.1781550.16423435X-RAY DIFFRACTION99.86

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